Sodium in PDB 4u9u: Crystal Structure of Nqrf Fad-Binding Domain From Vibrio Cholerae

The structure of Crystal Structure of Nqrf Fad-Binding Domain From Vibrio Cholerae, PDB code: 4u9u was solved by G.Fritz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.430, 89.070, 90.480, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 19.6

The structure of Crystal Structure of Nqrf Fad-Binding Domain From Vibrio Cholerae also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Nqrf Fad-Binding Domain From Vibrio Cholerae (pdb code 4u9u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Nqrf Fad-Binding Domain From Vibrio Cholerae, PDB code: 4u9u:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Nqrf Fad-Binding Domain From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Nqrf Fad-Binding Domain From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1504 b:38.3 occ:1.00 O A:ALA327 2.4 36.1 1.0 O A:HOH1826 2.5 42.3 1.0 O A:PHE333 2.5 31.7 1.0 O A:HOH1796 2.7 51.0 1.0 O A:ASN330 2.8 38.0 1.0 C A:ALA327 3.3 35.1 1.0 CA A:ALA327 3.6 30.5 1.0 C A:PHE333 3.7 27.1 1.0 C A:ASN330 3.8 33.8 1.0 CA A:ASP331 3.8 37.0 1.0 CB A:ALA327 3.9 30.5 1.0 CG1 A:VAL334 4.0 35.3 1.0 C A:ASP331 4.2 35.6 1.0 O A:HOH1775 4.2 46.2 1.0 O A:ASP331 4.2 39.5 1.0 N A:ASP331 4.2 31.3 1.0 N A:PHE333 4.3 28.3 1.0 N A:ALA328 4.5 35.2 1.0 CA A:PHE333 4.6 26.4 1.0 N A:VAL334 4.6 25.6 1.0 CA A:VAL334 4.7 30.6 1.0 N A:ASN330 4.8 35.5 1.0 CA A:ASN330 4.9 31.3 1.0 CA A:ALA328 4.9 34.0 1.0 CB A:VAL334 5.0 31.9 1.0 O A:LEU326 5.0 37.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Nqrf Fad-Binding Domain From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Nqrf Fad-Binding Domain From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1504 b:35.4 occ:1.00 O B:HOH1807 2.3 45.7 1.0 O B:PHE333 2.4 24.3 1.0 O B:HOH1847 2.5 62.1 1.0 O B:ALA327 2.5 34.4 1.0 O B:HOH1730 2.7 38.4 1.0 O B:ASN330 2.7 29.7 1.0 C B:ALA327 3.4 28.2 1.0 C B:PHE333 3.6 23.7 1.0 C B:ASN330 3.7 25.0 1.0 CA B:ALA327 3.7 24.8 1.0 CA B:ASP331 3.7 30.4 1.0 O B:ASP331 3.9 41.4 1.0 CB B:ALA327 4.0 25.2 1.0 C B:ASP331 4.0 34.3 1.0 N B:PHE333 4.1 22.3 1.0 N B:ASP331 4.2 31.1 1.0 CG1 B:VAL334 4.2 30.2 1.0 O B:HOH1662 4.3 40.4 1.0 CA B:PHE333 4.4 21.2 1.0 N B:VAL334 4.5 22.9 1.0 N B:ALA328 4.6 25.5 1.0 OD1 B:ASP331 4.7 45.5 0.6 N B:ASN332 4.7 28.3 1.0 CA B:VAL334 4.7 22.2 1.0 N B:ASN330 4.8 27.1 1.0 CA B:ASN330 4.8 23.8 1.0 CB B:ASP331 5.0 37.2 1.0 CB B:PHE333 5.0 21.6 1.0

J.Steuber, G.Vohl, M.S.Casutt, T.Vorburger, K.Diederichs, G.Fritz. Structure of the V. Cholerae Na+-Pumping Nadh:Quinone Oxidoreductase Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE14003